package edu.usc.epigenome.dnaase.script;

import java.io.BufferedReader;
import java.io.FileReader;
import java.util.ArrayList;
import java.util.List;

import org.kohsuke.args4j.Argument;
import org.kohsuke.args4j.CmdLineException;
import org.kohsuke.args4j.CmdLineParser;

public class OutputHetAndHomCytosineAndCpgInArray {

	/**
	 * @param args
	 */
	final private static String USAGE = "OutputHetAndHomCytosineAndCpgInArray [opts] snpArrayFileName fastaFileName ...";
	
	
	@Argument
	private List<String> stringArgs = new ArrayList<String>();
	
	public static void main(String[] args) throws Exception {
		// TODO Auto-generated method stub
		new OutputHetAndHomCytosineAndCpgInArray().doMain(args);
	}
	
	public void doMain(String[] args)
	throws Exception {

		CmdLineParser parser = new CmdLineParser(this);
		// if you have a wider console, you could increase the value;
		// here 80 is also the default
		parser.setUsageWidth(80);
		try
		{
			parser.parseArgument(args);
			if (stringArgs.size() < 2) throw new CmdLineException(USAGE);
		
		}
		catch (CmdLineException e)
		{
			System.err.println(e.getMessage());
			// print the list of available options
			parser.printUsage(System.err);
			System.err.println();
			return;
		}

		String snpFileName = stringArgs.remove(0);
		String fastaFileName = stringArgs.remove(0);
		BufferedReader br = new BufferedReader(new FileReader(snpFileName));
		BufferedReader brFastafile = new BufferedReader(new FileReader(fastaFileName));
		String line;
		while( (line = br.readLine()) != null){
			String[] tmpArray = line.split("\t");
			String chr = "chr" + tmpArray[1];
		}
		
	}

}
